Patterson, who tied a career high with five hits, led off the 14th with a drive to right off Gavin Floyd (5-5) for his third of the season. It was the fourth game-winning homer of his career.
Floyd started and went seven innings for Chicago in Wednesday's loss at Texas. He came out of the bullpen in the 13th, his first relief appearance since Aug. 24, 2007, against Boston.
Blue Jays left-hander Luis Perez (1-0) pitched 3 2-3 shutout innings for his first career win. The Blue Jays won back-to-back games for the first time since a season-high six-game winning streak from May 10-16.
Brent Lillibridge homered for the White Sox, who lost two in a row for the first time since a three-game losing streak from May 3-6.
Juan Rivera's bases-loaded double in the seventh gave the Blue Jays an 8-6 lead, but their struggling bullpen couldn't hold on.
Lillibridge tripled and scored on a passed ball in the eighth before the White Sox tied it against Frank Francisco in the ninth. Alexei Ramirez hit a one-out double down the right field line and, after Adam Dunn struck out, Paul Konerko drove in Ramirez with a bloop double to right that dropped in just in front of a sliding Bautista.
The blown save was the third of the season for Francisco, who has lost twice and has two blown saves in his past four games.
Toronto put runners at second and third with two outs in the bottom of the ninth but Rivera grounded out to pitcher Chris Sale to send the game to extra innings.
The White Sox put the winning run at third with one out in the 11th, but Perez struck out Dunn and got pinch-hitter Carlos Quentin to fly out.
The Blue Jays led 3-0 just three batters into the bottom of the first. Yunel Escobar walked, Patterson singled and Bautista lined a three-run homer to left-center.
Bautista reached the 20-homer mark in his 44th game, the fastest in Blue Jays history. George Bell needed 53 games to hit 20 homers in his 1987 MVP season.
No one has reached 20 homers more quickly than Barry Bonds. He did it in 39 games in 2001, when he hit an major league-record 73 home runs.
Lillibridge closed the gap with a two-run drive to left in the second, his fifth, but Toronto pulled ahead again by scoring twice in the third on Aaron Hill's two-run double.
Chicago took the lead with a three-run fifth, which began when Pierre reached on Hill's fielding error. Ramirez grounded out before Dunn laced an RBI single to center. Konerko doubled Dunn to third and A.J. Pierzynski followed with a two-run double to right.
Seeking to win consecutive starts for the first time since April 2 and 7, Chicago's Edwin Jackson ended up with a no-decision, allowing six runs and nine hits in 6 2-3 innings. He walked one and struck out seven.
NOTES: White Sox INF Gordon Beckham has a black eye but no broken bones or damaged vision after being hit under the left eye by a throw from the outfield Friday. Beckham said he hopes to return to the lineup by Monday. ... Litsch (shoulder) has been told not to throw at all for seven days after visiting doctors in Florida on Friday.